rs755596278
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 4P and 5B. PVS1_ModeratePP3_ModerateBS1_SupportingBS2
The NM_001348768.2(HECW2):c.-35-1G>A variant causes a splice acceptor change. The variant allele was found at a frequency of 0.00000975 in 1,435,750 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001348768.2 splice_acceptor
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HECW2 | NM_001348768.2 | c.-35-1G>A | splice_acceptor_variant | ENST00000644978.2 | |||
LOC105373822 | XR_923746.4 | n.44-2325C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HECW2 | ENST00000644978.2 | c.-35-1G>A | splice_acceptor_variant | NM_001348768.2 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000261 AC: 6AN: 229964Hom.: 0 AF XY: 0.0000403 AC XY: 5AN XY: 124166
GnomAD4 exome AF: 0.00000975 AC: 14AN: 1435750Hom.: 0 Cov.: 29 AF XY: 0.0000126 AC XY: 9AN XY: 712616
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Neurodevelopmental disorder with hypotonia, seizures, and absent language Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genomic Research Center, Shahid Beheshti University of Medical Sciences | Aug 07, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at